Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= curated2:Q89RB7 (404 letters) >FitnessBrowser__Miya:8500245 Length = 491 Score = 149 bits (376), Expect = 2e-40 Identities = 126/411 (30%), Positives = 191/411 (46%), Gaps = 48/411 (11%) Query: 25 VVLSRGEGVWVWDTDGNRYLDCLSAYSAVSQGHCHPKILAAMVEQ----AHRLTLTSRAF 80 +V+ EG + DTDG YLD +S+ GH HP++ AA+ Q AH L + Sbjct: 51 LVIGAAEGNRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGSE 110 Query: 81 HNDQLAPFYEEIAALTGSHKVLPMNSGAEAVESAIKSVRKWGYEVK---GVPDDQAEIIV 137 + +LA IA G +V +SG+ +VE A+K ++ + G + + Sbjct: 111 PSIELAARLAAIAP-QGLTRVFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFLS 169 Query: 138 CADNFHGRTLGIVGFSTDPETRGHFGPF--------APGFRIIPFGDAAAL--EQAITPN 187 + +HG T+G V + P +P PFG A + IT Sbjct: 170 LRNAYHGDTVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSCERECITHM 229 Query: 188 TVAF----------LVEP-IQGEAGVIIPPAGYFTKVRELCTANNVMLVLDEIQTGLGRT 236 F +VEP +QG AG+++ P G+ +VRELC + V LV DE+ G G+T Sbjct: 230 ETLFARHGHELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVAVGFGKT 289 Query: 237 GKLLAEQHEGIEADVTLLGKALAGGFYPVSAVLSNNEVLG-------TLRPGQHGSTFGG 289 G L A + EG+ D L K ++GG+ P++A L+ V LR HG T+ G Sbjct: 290 GTLFACEQEGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTFFHGHTYTG 349 Query: 290 NPLACAVARAAMRVLVEEGMIENAARQGARLLEGLKDIR-ANTVREVRGRGLMLAVELHP 348 NPLACA A A++ V EE ++E + ARL L +R V ++R RG+M +E+ Sbjct: 350 NPLACAAAIASLDVFEEERVMERLQPKIARLAARLDTLRDLPHVGDIRQRGVMTGIEMVR 409 Query: 349 EAGRARRYCEAL----------QGKGILAKDTHGHTIRIAPPLVITSDEVD 389 Y AL + +G++ + G + + PPL IT DE+D Sbjct: 410 NRATKEAYDLALRVGHRVTLEARRRGVIIRPL-GDVMVLMPPLSITDDEID 459 Lambda K H 0.319 0.136 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 524 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 404 Length of database: 491 Length adjustment: 32 Effective length of query: 372 Effective length of database: 459 Effective search space: 170748 Effective search space used: 170748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory